Clinicopathological analysis of nasopharyngeal tuberculosis.

BACKGROUND: The aim of this study is to examine the clinical and pathological attributes of nasopharyngeal tuberculosis. METHODS: We conducted a retrospective analysis of the clinicopathologic characteristics of nasopharyngeal tuberculosis in 14 patients. The medical records and imaging data obtained between March 2004 and February 2023 were scrutinized. During the pathological review, we classified the types of granulomatous inflammation and graded the extent of caseation. RESULTS: Results indicate a 100% female predominance, with chief complaints including hearing loss, postnasal drip, and nasal obstruction. Cervical lymphadenopathy occurred in 21.4% of patients. Chest radiograph abnormalities were found in 58.3%, with three showing active pulmonary tuberculosis. Endoscopic examination revealed three types of lesions, and CT/MRI findings correlated with gross lesions. A statistically significant association was found between lesion characteristics (bulging, ulcerative, necrotic) and pathology patterns (sarcoidosis-like, caseation). Bulging masses exhibited sarcoidosis-like patterns, while ulcerative/necrotic lesions were often associated with caseation. All lesions responded well to over six months of anti-tuberculosis medication, leading to favourable outcomes. CONCLUSION: We studied 14 cases of nasopharyngeal tuberculosis, mostly in females, with common ear and nose symptoms. Lesions were typically visible on nasopharyngeal endoscopy, and endoscopically bulging mass-like lesions had pathologically sarcoidosis-like granulomas. All patients had favourable outcomes.

Epithelial Antimicrobial Peptide/Protein and Cytokine Expression Profiles Obtained from Nasopharyngeal Swabs of SARS-CoV-2-Infected and Non-Infected Subjects.

Immune responses of the epithelia of the upper respiratory tract are likely crucial in early inhibition of the viral replication and finally clearance of SARS-CoV-2. We aimed to compare the expression profiles of antimicrobial peptides/proteins (AMPs) and related cytokines observed in the nasopharynx of SARS-CoV-2-infected patients and non-infected controls and to assess the associations between these parameters and COVID-19 patients' outcomes. We included 45 subjects who had tested positive for SARS-CoV-2 and 22 control subjects who had tested negative for SARS-CoV-2. Biomaterial for SARS-CoV-2 detection, as well as gene and protein expression studies, was obtained from all subjects using nasopharyngeal swabs which were performed a maximum of 7 days before inclusion in the study. Univariable and multivariable statistics were performed. When compared to the controls, the mRNA expression levels of human ß-defensin 1 (hBD-1), LL-37, and trappin-2 were significantly higher in specimens of nasopharyngeal swabs from COVID-19 patients. Protein expression of hBD-1 was also increased in the COVID-19 group. mRNA expression levels of interferon-É£ (IFN-É£), tumor necrosis factor- ɑ (TNF-ɑ), and interleukin-6 (IL-6) measured in SARS-CoV-2-infected patients were significantly higher than those observed in the controls, which could also be confirmed in the protein levels of IFN-É£ and IL-6. A significant correlation between mRNA and protein levels could be observed only for IL-6. Univariable analysis revealed that low IFN-É£ mRNA levels were associated with severe/fatal outcomes. The occurrence of COVID-19 pneumonia was significantly associated with lower expression levels of IL-6 mRNA, IFN-É£ mRNA, and TNF-ɑ mRNA. Concerning the severe/fatal outcomes, the multivariable logistic regression model revealed that none of the aforementioned parameters remained significant in the model. However, the logistic regression model revealed that higher TNF-ɑ mRNA expression was a significant independent predictor of absence of pneumonia [odds ratio: 0.35 (95% CI 0.14 to 0.88, p = 0.024)]. In conclusion, nasopharyngeal expression of AMPs (hBD-1, LL-37, and trappin-2) and cytokines (IL-6, IFN-É£, and TNF-ɑ) is upregulated in response to early SARS-CoV-2 infection, indicating that these AMPs and cytokines play a role in the local host defense against the virus. Upregulated nasopharyngeal TNF-ɑ mRNA expression during the early phase of SARS-CoV-2 infection was a significant independent predictor of the absence of COVID-19 pneumonia. Hence, high TNF-ɑ mRNA expression in the nasopharynx appears to be a protective factor for lung complications in COVID-19 patients.

Validation of Saliva as the Clinical Specimen Type for a University-Wide COVID-19 Surveillance Program.

At the beginning of the COVID-19 pandemic, the Georgia Institute of Technology made the decision to keep the university doors open for on-campus attendance. To manage COVID-19 infection rates, internal resources were applied to develop and implement a mass asymptomatic surveillance program. The objective was to identify infections early for proper follow-on verification testing, contact tracing, and quarantine/isolation as needed. Program success depended on frequent and voluntary sample collection from over 40,000 students, faculty, and staff personnel. At that time, the nasopharyngeal (NP) swab, not saliva, was the main accepted sample type for COVID-19 testing. However, due to collection discomfort and the inability to be self-collected, the NP swab was not feasible for voluntary and frequent self-collection. Therefore, saliva was selected as the clinical sample type and validated. A saliva collection kit and a sample processing and analysis workflow were developed. The results of a clinical sample-type comparison study between co-collected and matched NP swabs and saliva samples showed 96.7% positive agreement and 100% negative agreement. During the Fall 2020 and Spring 2021 semesters, 319,988 samples were collected and tested. The program resulted in maintaining a low overall mean positivity rate of 0.78% and 0.54% for the Fall 2020 and Spring 2021 semesters, respectively. For this high-throughput asymptomatic COVID-19 screening application, saliva was an exceptionally good sample type.

Case reports of persistent SARS-CoV-2 infection outline within-host viral evolution in immunocompromised patients.

BACKGROUND: SARS-CoV-2 is responsible for the ongoing global pandemic, and the continuous emergence of novel variants threatens fragile populations, such as immunocompromised patients. This subgroup of patients seems to be seriously affected by intrahost viral changes, as the pathogens, which are keen to cause replication inefficiency, affect the impaired immune system, preventing efficient clearance of the virus. Therefore, these patients may represent an optimal reservoir for the development of new circulating SARS-CoV-2 variants. The following study aimed to investigate genomic changes in SARS-CoV-2-positive immunocompromised patients over time. METHODS: SARS-CoV-2-positive nasopharyngeal swabs were collected at different time points for each patient (patient A and patient B), extracted and then analyzed through next-generation sequencing (NGS). The resulting sequences were examined to determine mutation frequencies, describing viral evolution over time. CASE PRESENTATION: Patient A was a 53-year-old patient with onco-hematological disease with prolonged infection lasting for 51 days from May 28th to July 18th, 2022. Three confirmed SARS-CoV-2-positive samples were collected on May 28th, June 15th and July 4th. Patient B was 75 years old and had onco-hematological disease with prolonged infection lasting for 146 days. Two confirmed positive SARS-CoV-2 samples were collected at the following time points: May 21st and August 18th. CONCLUSION: Heat map construction provided evidence of gain and/or loss of mutations over time for both patients, suggesting within-host genomic evolution of the virus. In addition, mutation polymorphisms and changes in the SARS-CoV-2 lineage were observed in Patient B. Sequence analysis revealed high mutational pattern variability, reflecting the high complexity of viral replication dynamics in fragile patients.

Oral SARS-CoV-2 host responses predict the early COVID-19 disease course.

Oral fluids provide ready detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and host responses. This study sought to evaluate relationships between oral virus, oral and systemic anti-SARS-CoV-2-specific antibodies, and symptoms. Oral fluids (saliva/throat wash (saliva/TW)) and serum were collected from asymptomatic and symptomatic, nasopharyngeal (NP) SARS-CoV-2 RT-qPCR+ human participants (n = 45). SARS-CoV-2 RT-qPCR and N-antigen detection by immunoblot and lateral flow assay (LFA) were performed. RT-qPCR for subgenomic RNA (sgRNA) was sequence confirmed. SARS-CoV-2-anti-S protein RBD LFA and ELISA assessed IgM and IgG responses. Structural analysis identified host salivary molecules analogous to SARS-CoV-2-N-antigen. At time of enrollment (baseline, BL), LFA-detected N-antigen in 86% of TW and was immunoblot-confirmed. However, only 3/17 were saliva/TW qPCR+ . Sixty percent of saliva and 83% of TW demonstrated persistent N-antigen at 4 weeks. N-antigen LFA signal in three anti-spike sero-negative participants suggested potential cross-detection of 4 structurally analogous salivary RNA binding proteins (alignment 19-29aa, RMSD 1-1.5 Angstroms). At enrollment, symptomatic participants demonstrated replication-associated sgRNA junctions, were IgG+ (94%/100% in saliva/TW), and IgM+ (63%/54%). At 4 weeks, SARS-CoV-2 IgG (100%/83%) and IgM (80%/67%) persisted. Oral and serum IgG correlated 100% with NP+ PCR status. Cough and fatigue severity (p = 0.010 and 0.018 respectively), and presence of weakness, nausea, and composite upper respiratory symptoms (p = 0.037, 0.005, and 0.017, respectively) were negatively associated with saliva IgM but not TW or serum IgM. Throat wash IgM levels were higher in women compared to men, although the association did not reach statistical significance (median: 290 (female) versus 0.697, p = 0.056). Important to transmission and disease course, oral viral replication and persistence showed clear relationships with select symptoms and early oral IgM responses during early infection. N-antigen cross-reactivity may reflect mimicry of structurally analogous host proteins.

High abundance of butyrate-producing bacteria in the naso-oropharynx of SARS-CoV-2-infected persons in an African population: implications for low disease severity.

BACKGROUND: The association of the oral microbiome with SARS-CoV-2 infections and disease progression has been documented in European, Asian, and American populations but not in Africa. METHODS: We conducted a study in Ghana to evaluate and compare the naso-oropharyngeal microbiome in SARS-CoV-2-infected and uninfected persons before (pre-vaccine) and after vaccine availability (post-vaccine) in the country. 16S rRNA V3-V4 variable region was sequenced and analysed from DNA extracted from naso-oropharyngeal swabs. RESULTS: Considering only the infection status, infected and uninfected groups had no difference in their within-group diversity and was evident in the study population pre- and post-vaccine availability. The introduction of vaccines reduced the diversity of the naso-oropharyngeal microbiome particularly among SARS-CoV-2 positive persons and, vaccinated individuals (both infected and uninfected) had higher microbial diversity compared to their unvaccinated counterparts. SARS-CoV-2-positive and -negative individuals were largely compositionally similar varying by 4-7% but considering vaccination*infection statuses, the genetic distance increased to 12% (P = 0.003) and was mainly influenced by vaccination. Common among the pre- and post-vaccine samples, Atopobium and Finegoldia were abundant in infected and uninfected individuals, respectively. Bacteria belonging to major butyrate-producing phyla, Bacillota (particularly class Clostridia) and Bacteroidota showed increased abundance more strikingly in infected individuals before vaccines were available. They reduced significantly after vaccines were introduced into the country with Fusobacterium and Lachnoanaerobaculum being the only common bacteria between pre-vaccine infected persons and vaccinated individuals, suggesting that natural infection and vaccination correlate with high abundance of short-chain fatty acids. CONCLUSION: Our results show, in an African cohort, the abundance of bacteria taxa known for their protective pathophysiological processes, especially during infection, suggesting that this population is protected against severe COVID-19. The immune-related roles of the members of Bacillota and Bacteroidota that were found associated with infection and vaccination require further studies, and how these may be linked to ethnicity, diet and age. We also recommend expansion of microbiome-disease association studies across Africa to identify possible bacterial-mediated therapeutics for emerging infections.

Retrospective analysis of the upper airway anatomy and Sella turcica morphology across different skeletal malocclusions: a computerized technique.

OBJECTIVE: This study aimed to investigate the normal volumetric space and variations in the measurements of different landmarks in adults with different skeletal relations of the maxilla and the mandible based on CBCT data. The study also analyses these landmarks to locate any correlations. BACKGROUND: Numerous studies in orthodontics have found a relationship between orthodontic treatment and changes in the anatomy and function of the airway. Severe changes in airway morphology can cause breathing difficulties, lower quality of life, and even result in life-threatening conditions such as obstructive sleep apnoea. Consequently, orthodontic diagnosis and treatment planning require a thorough understanding of the airway space and its function. METHODS: The present retrospective study was conducted using CBCT records of 120 adult patients, containing 40 samples of each skeletal class (20 males and 20 females). The boundaries were defined for the 3 major regions: the nasopharynx, the oropharynx, and the hypopharynx. Various measurements were recorded across these regions, as well as selective cephalometric landmarks. The obtained data was used to calculate average and standard deviation, while regression analysis was used to evaluate correlations and t-test was used to test statistical significance of gender differences. RESULTS: The results demonstrate that skeletal Class III individuals exhibit a reduced airway volume in the nasopharynx compared to other groups, whereas skeletal Class II individuals displayed a diminished airway volume in the hypopharynx. A strong correlation was observed for Sella turcica parameters. There were no significant differences in skeletal parameters across genders. Nasopharynx cavity volume demonstrated significant differences between skeletal Class I-Class III as well as between skeletal Class II-Class III. Hypopharynx cavity volume also demonstrated significant differences between skeletal Class I-Class II and between skeletal Class II-Class III. CONCLUSION: The major findings are the presence of a reduced nasopharyngeal volume in skeletal Class III malocclusions while skeletal Class II individuals displayed a diminished hypopharyngeal volume, making these critical areas to consider during the diagnostic and orthodontic treatment planning stages. This study also revealed a consistent correlation between Sella turcica parameters across various facial skeletal profiles, with skeletal Class II patients exhibiting a distinct pattern and skeletal Class I and Class III demonstrating an average relationship.

Comparison of RT-PCR cycle threshold values between individual and pooled SARS-CoV-2 infected nasopharyngeal swab specimens.

The molecular reverse transcription-polymerase chain reaction (RT-PCR) testing of respiratory tract swabs has become mandatory to confirm the diagnosis of coronavirus disease 2019 (COVID-19). However, RT-PCR tests are expensive, require standardized equipment, and relatively long testing times, and the sample pooling method has been introduced to solve this issue. The aim of this study was to compare the cycle threshold (Ct) values of the individual sample and pooled sample methods to assess how accurate the pooling method was. Repeat RT-PCR examinations were initially performed to confirm the Ct values for each sample before running the pooled test procedure. Sample extraction and amplification were performed in both assays to detect ORF1ab, N, and E genes with a cut-off point value of Ct <38. Overall, there was no difference in Ct values between individual sample and pooled sample groups at all concentrations (p=0.259) and for all pooled sizes. Only pooled size of five could detect the Ct value in the pooled samples for all concentration samples, including low-concentration sample (Ct values 36 to 38). This study highlighted that pooled RT-PCR testing strategy did not reduce the quality of individually measured RT-PCR Ct values. A pool size of five could provide a practical technique to expand the screening capacity of RT-PCR.

Association between real-time polymerase chain reaction cycle threshold value and clinical presentation in children with Bordetella pertussis.

BACKGROUND: The cycle threshold (Ct) value is inversely proportional to the number of copies of the target region in a sample, suggesting that a low Ct value indicates a high pathogen load. The relationship between Ct value and clinical presentation in children with pertussis is not well-defined. METHODS: We investigated the relationships between the Ct value of nasopharyngeal samples positive for Bordetella pertussis deoxyribonucleic acid via real-time polymerase chain reaction (PCR), collected from children on admission and their adult family members between May 2022 and March 2024 at Hangzhou Children's Hospital, China. The study focused on the correlation between Ct value and clinical presentation in children with pertussis. RESULTS: The Ct value was positively correlated with age (r = 0.362, P = 0.001). The mean Ct value for children with pertussis was 28.0 (range: 22.0-32.0), which was lower than the 32.0 (range: 30.0-34.0) observed in adults. Ct value was inversely correlated with length of stay, an indicator of disease severity (r = -0.356, P = 0.001). Logistic regression analyses revealed that both Ct value (OR: 0.891, 95% CI: 0.799-0.993, P = 0.036) and white blood cell count (OR: 1.127, 95% CI: 1.005-1.263, P = 0.040) were independently associated with severity of pertussis. CONCLUSIONS: Real-time PCR Ct values at initial diagnosis for pertussis may potentially predict severe disease outcomes in children.

Changes in the upper airway and its surrounding structures after bimaxillary surgery in patients with cleft-related Class III deformity.

OBJECTIVES: To compare upper airway changes following bimaxillary surgery for correction of Class III deformity between patients with unilateral cleft lip and palate (UCLP) and bilateral cleft lip and palate (BCLP) and to compare the preoperative and postoperative upper airway among patients with UCLP and BCLP to healthy controls. MATERIALS AND METHODS: Sixty adults with CLP-related skeletal Class III deformity (30 UCLP and 30 BCLP) who consecutively underwent bimaxillary surgery were studied retrospectively. Cone-beam computed tomography (CBCT) was performed before and after surgery to measure upper airway and movements of facial skeletal and surrounding structures. CBCT images from 30 noncleft skeletal Class I adults, matched by age, gender, and body mass index and without surgical intervention, served as controls. RESULTS: After surgery, the volume of the nasopharynx increased in patients with CLP (both P < .001). Patients with CLP did not differ from controls in postoperative volume of the nasopharynx or oropharynx. However, the nasal cavity differed significantly between patients with CLP and controls (P < .001). CONCLUSIONS: After bimaxillary surgery, the nasal cavity of patients with CLP differed significantly compared with the controls. Volumes of the nasopharynx and oropharynx did not differ between patients with CLP after surgery and controls.

[Antimicrobial in vitro effects of eight essential oils on Pasteurella multocida and Mannheimia haemolytica from nasopharyngeal swab samples of fattening calves]. / Antimikrobielle in-vitro-Wirkung acht ätherischer Öle auf Pasteurella multocida und Mannheimia haemolytica aus Nasenrachentupferproben von Mastkälbern.

INTRODUCTION: Essential oils are secondary metabolites of aromatic plants and are used in phytotherapy to treat various diseases. In the present study, eight selected essential oils - ajwain oil (Trachyspermum ammi L.), fennel oil (Foeniculum vulgare Mill. subsp. vulgare var. vulgare), thyme oil chemotype (ct.) thymol (Thymus vulgaris L.), tea tree oil (Melaleuca alternifolia Cheel.), oregano oil (Origanum vulgare L.), mountain savory oil (Satureja montana L.), lemongrass oil (Cymbopogon citratus (DC.) Stapf.) and eucalyptus oil (Eucalyptus globulus Labill.) -were examined for their antibacterial effect against Pasteurella (P.) multocida and Mannheimia (M.) haemolytica isolates from deep nasopharyngeal swab samples of fattening calves using agar diffusion and microdilution. All eight essential oils were effective against the tested isolates. Lemongrass oil proved to be the most potent of all eight essential oils, while fennel oil was only weakly effective. Different antimicrobial effects were observed between the two research methods. The effectiveness of ajwain, thyme, oregano and mountain savory oils was comparable in agar diffusion. However, this could not be reproduced using the microdilution method. P. multocida was found to be more sensitive to all essential oils tested than M. haemolytica. This study shows that the tested essential oils have antimicrobial in-vitro effects on P. multocida and M. haemolytica isolates and that the examination method is associated with the test result.

INTRODUCTION: Les huiles essentielles sont des métabolites secondaires de plantes aromatiques et sont utilisées en phytothérapie pour le traitement de différentes maladies. Dans la présente étude, huit huiles essentielles sélectionnées ­ huile d'ajowan (Trachyspermum ammi L.), huile de fenouil (Foeniculum vulgare Mill. subsp. vulgare var. vulgare), huile de thym chémotype (ct.) thymol (Thymus vulgaris L.), huile d'arbre à thé (Melaleuca alternifolia Cheel.), huile d'origan (Origanum vulgare L.), huile de sarriette de montagne (Satureja montana L. ), huile de citronnelle (Cymbopogon citratus (DC.) Stapf.) et huile d'eucalyptus (Eucalyptus globulus Labill.) ­ ont été étudiées par diffusion sur gélose et microdilution pour leur effet antibactérien sur des isolats de Pasteurella (P.) multocida et de Mannheimia (M.) haemolytica provenant d'échantillons d'écouvillons nasaux profonds de veaux d'engraissement. Les huit huiles essentielles se sont révélées efficaces sur les isolats testés. L'huile de citronnelle s'est avérée être la plus puissante des huit huiles essentielles, tandis que l'huile de fenouil n'était que faiblement efficace. Des effets différents ont été observés entre les deux méthodes de recherche utilisées. Par exemple, l'efficacité des huiles d'ajowan, de thym, d'origan et de sarriette de montagne était comparable dans la diffusion sur gélose. Cependant, cela n>a pas pu être reproduit avec la méthode de microdilution. P. multocida s'est révélée plus sensible que M. haemolytica à toutes les huiles essentielles testées. Cette étude montre premièrement que les huiles essentielles testées ont une efficacité antimicrobienne in vitro sur des isolats cliniques de P. multocida et de M. haemolytica. Deuxièmement, elle montre que la méthode d'examen est associée au résultat du test.

SARS-CoV-2 not Detected in the Nasopharyngeal Sample but in Bronchoalveolar Lavage Fluid.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection typically relies on reverse transcription-polymerase chain reaction (RT-PCR) technology. However, there is a certain rate of missed detection of SARS-CoV-2 in nasopharyngeal samples, particularly among immunosuppressed individuals. METHODS: In this case, SARS-CoV-2 was detected in nasopharyngeal swabs and bronchoalveolar lavage fluid (BALF) using RT-PCR. Pulmonary imaging was performed using computed tomography (CT). Patient clinical data were retrieved from the Laboratory Information System (LIS). RESULTS: SARS-CoV-2 was negative in two nasopharyngeal tests of the patient, but was finally detected in BALF, confirming that the lung lesions were infected by SARS-CoV-2. CONCLUSIONS: In the post-epidemic era, it is necessary to use BALF to identify SARS-CoV-2 infection in cases where other factors have been ruled out in immunosuppressed individuals with pulmonary infections, especially when the nasopharyngeal test yields a negative result.

Æ©S COVID-19 is a rapid high throughput and sensitive one-step quadruplex real-time RT-PCR assay.

Real-time reverse transcription polymerase chain reaction (RT-PCR), a standard method recommended for the diagnosis of coronavirus disease 2019 (COVID-19) requires 2-4 h to get the result. Although antigen test kit (ATK) is used for COVID-19 screening within 15-30 min, the drawback is its limited sensitivity. Hence, a rapid one-step quadruplex real-time RT-PCR assay: termed Æ©S COVID-19 targeting ORF1ab, ORF3a, and N genes of SARS-CoV-2; and Avocado sunblotch viroid (ASBVd) as an internal control was developed. Based on strategies including designing high melting temperature primers with short amplicons, applying a fast ramp rate, minimizing hold time, and reducing the range between denaturation and annealing/extension temperatures; the assay could be accomplished within 25 min. The limit of detection of ORF1ab, ORF3a, and N genes were 1.835, 1.310, and 1 copy/reaction, respectively. Validation was performed in 205 combined nasopharyngeal and oropharyngeal swabs. The sensitivity, specificity, positive predictive value, and negative predictive value were 92.8%, 100%, 100%, and 97.1%, respectively with 96.7% accuracy. Cohen's Kappa was 0.93. The newly developed rapid real-time RT-PCR assay was highly sensitive, specific, and fast, making it suitable for use as an alternative method to support laboratory diagnosis of COVID-19 in outpatient and emergency departments.

Epidemiology and genetic characterization of human parainfluenza virus-1 infection in pediatric patients from Hangzhou China, 2021-2022.

BACKGROUND: Human parainfluenza virus-1 (HPIV-1) is a notable pathogen instigating acute respiratory tract infections in children. The article is to elucidate the epidemiological and genetic characteristics of HPIV-1 circulating in Hangzhou during the period of 2021-2022. METHODS: A cohort of 2360 nasopharyngeal swabs were amassed and subsequently examined via RT-PCR, with HPIV-1 positive samples undergoing P gene sequencing. RESULTS: The highest HPIV-1 infection rates were found in children aged between 3 and 6 years. A pronounced positive rate persisted through the latter half of 2021, with a notable decline observed in the initial half of 2022. All HPIV-1 strains could be clustered into 2 groups: Cluster 1, with strains similar to those found in Japan (LC764865, LC764864), and Cluster 2, with strains similar to the Beijing strain (MW575643). CONCLUSION: In conclusion, our study contributes to the comprehensive data on the epidemiological and genetic characteristics of HPIV-1 in pediatric patients from Hangzhou, post the COVID-19 peak.

Development and validation of predictive models for skeletal malocclusion classification using airway and cephalometric landmarks.

OBJECTIVE: This study aimed to develop a deep learning model to predict skeletal malocclusions with an acceptable level of accuracy using airway and cephalometric landmark values obtained from analyzing different CBCT images. BACKGROUND: In orthodontics, multitudinous studies have reported the correlation between orthodontic treatment and changes in the anatomy as well as the functioning of the airway. Typically, the values obtained from various measurements of cephalometric landmarks are used to determine skeletal class based on the interpretation an orthodontist experiences, which sometimes may not be accurate. METHODS: Samples of skeletal anatomical data were retrospectively obtained and recorded in Digital Imaging and Communications in Medicine (DICOM) file format. The DICOM files were used to reconstruct 3D models using 3DSlicer (slicer.org) by thresholding airway regions to build up 3D polygon models of airway regions for each sample. The 3D models were measured for different landmarks that included measurements across the nasopharynx, the oropharynx, and the hypopharynx. Male and female subjects were combined as one data set to develop supervised learning models. These measurements were utilized to build 7 artificial intelligence-based supervised learning models. RESULTS: The supervised learning model with the best accuracy was Random Forest, with a value of 0.74. All the other models were lower in terms of their accuracy. The recall scores for Class I, II, and III malocclusions were 0.71, 0.69, and 0.77, respectively, which represented the total number of actual positive cases predicted correctly, making the sensitivity of the model high. CONCLUSION: In this study, it is observed that the Random Forest model was the most accurate model for predicting the skeletal malocclusion based on various airway and cephalometric landmarks.

An at-home and electro-free COVID-19 rapid test based on colorimetric RT-LAMP.

INTRODUCTION: In the fight against virus-caused pandemics like COVID-19, diagnostic tests based on RT-qPCR are essential, but they are sometimes limited by their dependence on expensive, specialized equipment and skilled personnel. Consequently, an alternative nucleic acid detection technique that overcomes these restrictions, called loop-mediated isothermal amplification following reverse transcription (RT-LAMP), has been broadly investigated. Nevertheless, the developed RT-LAMP assays for SARS-CoV-2 detection still require laboratory devices and electrical power, limiting their widespread use as rapid home tests. This work developed a flexible RT-LAMP assay that gets beyond the drawbacks of the available isothermal LAMP-based SARS-CoV-2 detection, establishing a simple and effective at-home diagnostic tool for COVID-19. METHODOLOGY: A multiplex direct RT-LAMP assay, modified from the previously developed test was applied to simultaneously identify the two genes of SARS-CoV-2. We used a colorimetric readout, lyophilized reagents, and benchmarked an electro-free and micropipette-free method that enables sensitive and specific detection of SARS-CoV-2 in home settings. RESULTS: Forty-one nasopharyngeal swab samples were tested using the developed home-testing RT-LAMP (HT-LAMP) assay, showing 100% agreement with the RT-qPCR results. CONCLUSIONS: This is the first electrically independent RT-LAMP assay successfully developed for SARS-CoV-2 detection in a home setting. Our HT-LAMP assay is thus an important development for diagnosing COVID-19 or any other infectious pandemic on a population scale.

An alternative colorimetric RT-LAMP assay for the rapid detection of SARS-CoV-2: development and validation in Thailand.

INTRODUCTION: COVID-19, an emerging infectious disease caused by SARS-CoV-2, continues to be a global public health threat. The development of a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) can extend the availability of simple, reliable molecular tests for the rapid detection of COVID-19. METHODOLOGY: The RT-LAMP assay was developed using a new primer set targeting a portion of SARS-CoV-2 orf8. The method was validated at 63 ºC for 60 minutes with naked-eye visualization of the color change. The clinical performance was compared to a real-time reverse transcription-polymerase chain reaction (rtRT-PCR) using 273 RNA samples extracted from nasopharyngeal swab specimens. RESULTS: The developed RT-LAMP was specific to SARS-CoV-2 with a limit of detection at 15 RNA copies per reaction. The assay demonstrated diagnostic accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of 90.48% (95% CI: 86.36-93.68%), 87.00% (95% CI: 81.53-91.33%), 100% (95% CI: 95.07-100%), 100% (95% CI: not available), and 73.74% (95% CI: 66.22-80.07%), respectively, compared to the rtRT-PCR. The greatest sensitivity of 98.03% (95% CI: 94.34-99.59%) was demonstrated in samples with the cycle threshold (Ct) values < 30 cycles. CONCLUSIONS: The RT-LAMP method in this study showed good performance. The assay can increase the scope of laboratory testing for rapidly detecting SARS-CoV-2 in Thailand. Due to a decrease in COVID-19 cases, its application is beneficial when commercial alternatives are unavailable.

Estimating pneumococcal carriage dynamics in adults living with HIV in a mature infant pneumococcal conjugate vaccine programme in Malawi, a modelling study.

BACKGROUND: Adults living with human immunodeficiency virus (ALWHIV) receiving antiretroviral therapy (ART) exhibit higher pneumococcal carriage prevalence than adults without HIV (HIV-). To assess factors influencing high pneumococcal carriage in ALWHIV, we estimated pneumococcal carriage acquisition and clearance rates in a high transmission and disease-burdened setting at least 10 years after introducing infant PCV13 in routine immunisation. METHODS: We collected longitudinal nasopharyngeal swabs from individuals aged 18-45 in Blantyre, Malawi. The study group included both HIV- individuals and those living with HIV, categorised based on ART duration as either exceeding 1 year (ART > 1y) or less than 3 months (ART < 3 m). Samples were collected at baseline and then weekly for 16 visits. To detect pneumococcal carriage, we used classical culture microbiology, and to determine pneumococcal serotypes, we used latex agglutination. We modelled trajectories of serotype colonisation using multi-state Markov models to capture pneumococcal carriage dynamics, adjusting for age, sex, number of under 5 year old (< 5y) children, social economic status (SES), and seasonality. RESULTS: We enrolled 195 adults, 65 adults in each of the study groups. 51.8% were females, 25.6% lived with more than one child under 5 years old, and 41.6% lived in low socioeconomic areas. The median age was 33 years (IQR 25-37 years). The baseline pneumococcal carriage prevalence of all serotypes was 31.3%, with non-PCV13 serotypes (NVT) at 26.2% and PCV13 serotypes (VT) at 5.1%. In a multivariate longitudinal analysis, pneumococcal carriage acquisition was higher in females than males (hazard ratio [HR], NVT [1.53]; VT [1.96]). It was also higher in low than high SES (NVT [1.38]; VT [2.06]), in adults living with 2 + than 1 child < 5y (VT [1.78]), and in ALWHIV on ART > 1y than HIV- adults (NVT [1.43]). Moreover, ALWHIV on ART > 1y cleared pneumococci slower than HIV- adults ([0.65]). Residual VT 19F and 3 were highly acquired, although NVT remained dominant. CONCLUSIONS: The disproportionately high point prevalence of pneumococcal carriage in ALWHIV on ART > 1y is likely due to impaired nasopharyngeal clearance, which results in prolonged carriage. Our findings provide baseline estimates for comparing pneumococcal carriage dynamics after implementing new PCV strategies in ALWHIV.

Pathogen kinetics and detection by next-generation sequencing in pediatric complicated pneumonia.

Pediatric pneumonia can be severe and result in empyema. Next-generation sequencing (NGS) may broadly detect pathogens though, optimal timing and impact of sample type on diagnostic yield is unknown. This is a prospective, single-center pilot study of children aged 3 months through 17 years admitted to the PICU with a primary diagnosis of complicated pneumonia. Plasma, endotracheal, nasopharyngeal, and pleural fluid samples were collected at three time points during hospitalization. After nucleic acid extraction, combined libraries were enriched with an NGS enrichment panel kit (RPIP, Illumina), sequenced and quantitative organism detections were analyzed. NGS identified the same bacterial pathogen as traditional testing in all samples, regardless of antibiotic pre-treatment or time collected. Conventional culture methods only identified the pathogen reliably in invasively obtained pleural fluid or endotracheal aspirates. Future application of NGS may allow for non-invasive pathogen detection at a broader range of time points and more targeted antibiotic coverage.

Host and environmental factors shape upper airway microbiota and respiratory health across the human lifespan.

Our understanding of the normal variation in the upper respiratory tract (URT) microbiota across the human lifespan and how these relate to host, environment, and health is limited. We studied the microbiota of 3,104 saliva (<10 year-olds)/oropharynx (≥10 year-olds) and 2,485 nasopharynx samples of 3,160 Dutch individuals 0-87 years of age, participating in a cross-sectional population-wide study (PIENTER-3) using 16S-rRNA sequencing. The microbiota composition was strongly related to age, especially in the nasopharynx, with maturation occurring throughout childhood and adolescence. Clear niche- and age-specific associations were found between the microbiota composition and host/environmental factors and health outcomes. Among others, social interaction, sex, and season were associated with the nasopharyngeal microbial community. By contrast, the oral microbiota was more related to antibiotics, tobacco, and alcohol use. We present an atlas of the URT microbiota across the lifespan in association with environment and health, establishing a baseline for future research.